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Potential of Bacillus paramycoides hydrolase to degrade propiconazole Cover

Potential of Bacillus paramycoides hydrolase to degrade propiconazole

Archives of Industrial Hygiene and Toxicology
Volume 77 (2026): Issue 1 (March 2026)
By: Muhammad Naveed,  Maida Salah Ud Din,  Tariq Aziz,  Rida Naveed,  Daochen Zhu,  Maha Alharbi and  Ashwag Shami  
Open Access
|Mar 2026
Figures & tables

Figures & Tables

Figure 1

The phylogenetic tree for hydrolase

Figure 2

3D structure of hydrolase generated by the SWISS-MODEL tool. The purple region shows the Hsp70 chaperone of E. coli for the production of stable conjugate protein complex

Figure 3

Ramachandran plot of hydrolase from Bacillus paramycoides

Figure 4

Active site prediction with Discovery Studio

Figure 5

Interaction between hydrolase and (2R,4S)-2-(2,4-dichlorophenyl)-4-propyl-2-[(1H-1,2,4-triazol-1-yl)methyl]-1,3-dioxolane complex 1 visualised with PyMOL

Figure 6

Interaction between hydrolase and 1-[[2-(2,4-dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole complex 2 visualised with PyMOL

Figure 7

Interaction between hydrolase and 1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole complex 3 visualised with PyMOL

Figure 8

Interaction between hydrolase and propiconazole 4,4’-dihydroxybiphenyl complex 4 visualised with PyMOL

Figure 9

Interaction between hydrolase and propiconazole hydrochloride complex 5 visualised with PyMOL

Figure 10

Interaction between hydrolase and propiconazole-d7 complex 6 visualised with PyMOL

Figure 11

Interaction between hydrolase and propiconazole complex 7 visualised with PyMOL

Figure 12

Interaction between hydrolase and propiconazole TP1 complex 8 visualised with PyMOL

Figure 13

Mutated structure of hydrolase from Bacillus paramycoides

Figure 14

Interaction between hydrolase and propiconazole TP1. The ligand is positioned within the active site and stabilised by key catalytic residues, including His66, His67, and Trp92. Additional residues such as Phe13, Val15, Lys130, and Thr131 contribute through hydrophobic contacts and hydrogen bonding. Green lines represent hydrogen bonds, magenta lines hydrophobic and π–π interactions

Figure 15

Interaction between mutated hydrolase and 1-[[2-(2,4-dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole

Figure 16

Interaction between mutated hydrolase and 1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl] methyl]-1,2,4-triazole

Figure 17

Protein–ligand complex analysis in molecular dynamics simulation. A) Root mean square deviation (RMSD) shows the overall structural stability of the complex by tracking backbone fluctuations over time. B) Radius of gyration (Rg) shows the compactness and structural integrity of the protein; consistent Rg values suggest a stable and well-folded conformation. C) Root mean square fluctuation (RMSF) highlights residue-specific flexibility, identifying regions with higher mobility such as loops, binding pockets, or terminal ends. D) Principal component analysis (PCA) illustrates dominant collective motions and major conformational transitions of the complex, helping to visualise large-scale structural dynamics that influence ligand binding and enzyme function

Figure 18

Distance analysis between the ligand and key protein residues in molecular dynamics simulation. A) Ligand-catalytic residue distances are consistently short (0.98–2.89 Å), which indicates stable interactions, essential for catalytic activity and effective binding. B) Significantly larger separation between the ligand and selected, non-catalytic residues (25.83–28.99 Å) confirms that these residues do not directly participate in ligand interaction and remain structurally distant throughout the simulation

Secondary structure predicted with SOPMA

Alpha helixExtended strandsBeta turnsRandom coils
41.64 %19.24 %7.57 %31.55 %

Docking and interaction study of hydrolase with the best three propiconazole derivatives

PollutantsDocking energies (kcal/mol)Amino acid residuesDistance between interacting amino acid residues (Å)Type of bond interaction
Propiconazole TP1−7.4HIS66, TRP92, HIS67, VAL15, THR131, PHE13, LYS1302.84, 2.93, 3.14, 4.26, 5.01, 4.92, 4.67, 4.99, 5.23, 3.02Alkyl, pi-alkyl, conventional, Pi-Pi T-shaped, hydrogen bonds, Van der Waals forces
1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl] methyl]-1,2,4-triazole−7.1HIS67, HIS66, TRP92, ILE192, ALA165, HIS164, HIS653.94, 4.85, 4.71, 4.31, 4.57, 3.68Pi-lone pair, Pi-alkyl, Pi-Pi T-shaped, Van der Waals forces
1-[[2-(2,4-Dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole−7.1ILE194, HIS164, ASP183, ALA165, TYR139 HIS67, HIS66, HIS65,4.42, 2.95, 2.75, 4.44, 5.50, 5.41, 3.76, 4.82, 2.70, 3.61, 2.08Alkyl, pi-alkyl, conventional, Pi-Pi T-shaped, carbon, Waals forces hydrogen bonds, Van der

Active site prediction with Discovery Studio

SitesDimensions XYZPoint Count
Site 112.779000 / 8.882247 / −8.6105735407
Site 2−3.971000 / −3.617753 / 1.1394271330
Site 3−5.721000 / 12.132247 / −2.110573708

Selected propiconazole and its derivatives

Ser. no.Compound namePubChem CIDFormulaStructure
1(2R,4S)-2-(2,4-Dichlorophenyl)- 4-propyl-2-[(1H-1,2,4-triazol-1-yl) methyl]-1,3-dioxolane679162C15H17Cl2N3O2
21-[[(2S,4S)-2-(2,4-dichlorophenyl)- 4-propyl-1,3-dioxolan-2-yl]methyl]- 1,2,4-triazole679164C15H17Cl2N3O2
31-[[2-(2,4-Dichlorophenyl)-4- (2,2,3,3,3-pentadeuteriopropyl)-1,3- dioxolan-2-yl]methyl]-1,2,4-triazole129318213C15H17Cl2N3O2
4Hispor156985C24H26Cl2N6O4
5Propiconazole 4,4′-dihydroxybiphenyl86643422C27H27Cl2N3O4
6Propiconazole hydrochloride129773016C15H18Cl3N3O2
7Propiconazole TP1155884399C13H11Cl2N3O4
8Propiconazole TP2703104C10H9Cl2N3O
9Propiconazole-(phenyl-d3)124202653C15H17Cl2N3O2
10Propiconazole43234C15H17Cl2N3O2
11Propiconazole-d771751781C15H17Cl2N3O2

Physiochemical characterisation of the Bacillus paramycoides hydrolase enzyme

Amino acids (N)932
Molecular weight1869.85
Theoretical pI5.18
Negatively charged residues (N)127
Positively charged resides (N)90
FormulaC4492H7230N1258O1390S24
Total No. of atoms14394
Ext. coefficient26025
Estimated half-life30 h (mammalian reticulocytes, in vitro) >20 h (yeast, in vivo) >10 h (Escherichia coli, in vivo)
Instability index38.07
Aliphatic index100.71
Grand average of hydropathicity−0.095

Binding energies and types of intermolecular interactions of compounds with hydrolase

CompoundsMolecular weight (g/mol)Energy (kcal/mol)
1-[[(2S,4S)-2-(2,4-dichlorophenyl)-4-propyl-1,3-dioxolan-2-yl] methyl]-1,2,4-triazole342.2−6.8
Propiconazole TP1344.15−6.6
1-[[2-(2,4-Dichlorophenyl)-4-(2,2,3,3,3-pentadeuteriopropyl)-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole347.2−6.2
Propiconazole342.2−6.2
(2R,4S)-2-(2,4-Dichlorophenyl)-4-propyl-2-[(1H-1,2,4-triazol-1-yl)methyl]-1,3-dioxolane342.2−6.1
Hispor533.4−6.1
Propiconazole-d7349.3−6.0
Propiconazole 4,4′-dihydroxybiphenyl528.4−5.9
Propiconazole hydrochloride378.7−5.9
Propiconazole-(phenyl-d3)345.2−5.8
Propiconazole TP2258.1−5.7

Identified mutations and classification of mutants in silico

Metallo-ß-lactamase fold metallo-hydrolase by speciesAccession numberAmino acid substitutedMutation positionAmino acid replaced withI-mutant resultsMU-PRO resultPHD-SNP resultsSIFT results
Bacillus paramycoidesWP_178938973.1D151EIncreaseIncreaseNeutralNeutral
Bacillus cereusWP_193645052.1N82KDecreaseDecreaseDeleteriousDeleterious
Bacillus mycoidesWP_215554119.1V238MDecreaseDecreaseDeleteriousNeutral
Bacillus thuringiensisWP_264539129.1D123GDecreaseDecreaseNeutralDeleterious
Bacillus nitratireducensWP_044737773.1L312WDecreaseIncreaseNeutralDeleterious
Bacillus sp. CDB3WP_128853480.1H47QDecreaseIncreaseDeleteriousNeutral
Bacillus sp. TH12WP_201056898.1A119VIncreaseIncreaseNeutralNeutral
Bacillus sp. NP247WP_219920057.1V50ADecreaseDecreaseDeleteriousDeleterious
Bacillus sp. MYb209WP_105584583.1T33IDecreaseDecreaseNeutralNeutral
Bacillus toyonensisWP_097999873.1K108RDecreaseDecreaseNeutralNeutral

MM/PBSA complex–receptor–ligand energy decomposition

Energy componentAverageSDSEM
VDWAALS−39.66685.98131.8915
EEL−0.60352.22590.7039
EPB12.92975.55571.7569
ENPOLAR−21.18053.22401.0195
EDISPER41.76994.09501.2950
DELTA G gas−40.27035.90551.8675
DELTA G solv33.51926.05841.9158
DELTA TOTAL−6.75117.04642.2283

MM/GBSA complex–receptor–ligand energy decomposition

Energy componentAverageSDSEM
VDWAALS−39.66685.98131.8915
EEL−0.60352.22590.7039
EGB8.05172.98880.9451
ESURF−3.69380.54310.1718
DELTA G gas−40.27035.90551.8675
DELTA G solv4.35793.19381.0100
DELTA TOTAL−35.91246.46292.0437
DOI: https://doi.org/10.2478/aiht-2026-77-4001 | Journal eISSN: 1848-6312 | Journal ISSN: 0004-1254
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Language: English, Croatian, Slovenian
Page range: 9 - 20
Submitted on: May 1, 2025
Accepted on: Mar 1, 2026
Published on: Mar 30, 2026
Published by: Institute for Medical Research and Occupational Health
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
bioremediation,
environmental toxicology,
hydrolase enzymes,
molecular docking,
propiconazole degradation
Related subjects:
Medicine,
Basic medical science,
Basic medical science, other

© 2026 Muhammad Naveed, Maida Salah Ud Din, Tariq Aziz, Rida Naveed, Daochen Zhu, Maha Alharbi, Ashwag Shami, published by Institute for Medical Research and Occupational Health
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 77 (2026): Issue 1 (March 2026)
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